\hypertarget{classCharmm}{\section{\-Charmm \-Class \-Reference}
\label{classCharmm}\index{\-Charmm@{\-Charmm}}
}
\subsection*{\-Public \-Member \-Functions}
\begin{DoxyCompactItemize}
\item 
\hypertarget{classCharmm_a117a30a5b04bd0e23dc928fc810a97cf}{{\bfseries constructor} ?conf?}\label{classCharmm_a117a30a5b04bd0e23dc928fc810a97cf}

\item 
\hypertarget{classCharmm_a21b0cfe35ff6e039068346a3e38fae49}{{\bfseries start} ?config?}\label{classCharmm_a21b0cfe35ff6e039068346a3e38fae49}

\item 
\hypertarget{classCharmm_a59f8d57b7b97e84c3ec1d17b9fe5d769}{{\bfseries send\-Cmd} cmd}\label{classCharmm_a59f8d57b7b97e84c3ec1d17b9fe5d769}

\item 
\hypertarget{classCharmm_a9a439e1cb07b033fd702d33cab2a8aac}{{\bfseries do} cmds?until??condition?}\label{classCharmm_a9a439e1cb07b033fd702d33cab2a8aac}

\item 
\hypertarget{classCharmm_a31a89037ecdc62b92776d89a0d9f378a}{{\bfseries abort}}\label{classCharmm_a31a89037ecdc62b92776d89a0d9f378a}

\item 
\hypertarget{classCharmm_a3b94c792835ac1998925388f49630cdd}{{\bfseries setup} config}\label{classCharmm_a3b94c792835ac1998925388f49630cdd}

\item 
\hypertarget{classCharmm_a112fa9f5c922f6b950d8d982b1d8ac44}{{\bfseries autosetup}}\label{classCharmm_a112fa9f5c922f6b950d8d982b1d8ac44}

\item 
\hypertarget{classCharmm_a612ebbfd4873555f2035107fbe423ded}{{\bfseries print\-Config}}\label{classCharmm_a612ebbfd4873555f2035107fbe423ded}

\item 
\hypertarget{classCharmm_a6bd7757d30b569b5e87222d45d8600e4}{{\bfseries gen\-I\-C}}\label{classCharmm_a6bd7757d30b569b5e87222d45d8600e4}

\item 
\hypertarget{classCharmm_a9a13af20df04d01480acd6bfd0d72acc}{{\bfseries refill\-I\-C}}\label{classCharmm_a9a13af20df04d01480acd6bfd0d72acc}

\item 
\hypertarget{classCharmm_ace99d4aada436fc85cf3135aaf0a7a54}{{\bfseries get\-I\-C}}\label{classCharmm_ace99d4aada436fc85cf3135aaf0a7a54}

\item 
\hypertarget{classCharmm_ac0c9444613ba648f2a9b471379857a4c}{{\bfseries get\-Energy}}\label{classCharmm_ac0c9444613ba648f2a9b471379857a4c}

\item 
\hypertarget{classCharmm_afec028879009479294264a3ce9ab6fb5}{{\bfseries minimize} type nstep}\label{classCharmm_afec028879009479294264a3ce9ab6fb5}

\item 
\hypertarget{classCharmm_a90ab36107aa00cda3369bcefbccaf2c5}{{\bfseries turnon} module args}\label{classCharmm_a90ab36107aa00cda3369bcefbccaf2c5}

\item 
\hypertarget{classCharmm_ae729b15191f7c86c5f8dd14daef1c4a4}{{\bfseries turnoff} module}\label{classCharmm_ae729b15191f7c86c5f8dd14daef1c4a4}

\item 
\hypertarget{classCharmm_a3c5805f2b89fa7e6bec9d038e9ea56de}{{\bfseries move} object args}\label{classCharmm_a3c5805f2b89fa7e6bec9d038e9ea56de}

\item 
\hypertarget{classCharmm_a047a833f6706b6cc1154a62eaa4df146}{{\bfseries move2} object args}\label{classCharmm_a047a833f6706b6cc1154a62eaa4df146}

\item 
\hypertarget{classCharmm_a46c2c6f2c122341f0abecfb43bca775e}{{\bfseries align} object args}\label{classCharmm_a46c2c6f2c122341f0abecfb43bca775e}

\item 
\hypertarget{classCharmm_a3e50a6682431941d38b6647e98d453b7}{{\bfseries tilt} object args}\label{classCharmm_a3e50a6682431941d38b6647e98d453b7}

\item 
\hypertarget{classCharmm_a6d021e0f4c3d907f7f1af98117122cd9}{{\bfseries rotate2} object args}\label{classCharmm_a6d021e0f4c3d907f7f1af98117122cd9}

\item 
\hypertarget{classCharmm_a875d70d859224d8d08ae7a669883adfe}{{\bfseries rotate} object args}\label{classCharmm_a875d70d859224d8d08ae7a669883adfe}

\item 
\hypertarget{classCharmm_a3bb6a424f25353b753cc72b6ee8ce793}{{\bfseries get\-C\-O\-M} object}\label{classCharmm_a3bb6a424f25353b753cc72b6ee8ce793}

\item 
\hypertarget{classCharmm_a29e52529deb77a08f92dda07b1cd4cd7}{{\bfseries get\-Orientation} object}\label{classCharmm_a29e52529deb77a08f92dda07b1cd4cd7}

\item 
\hypertarget{classCharmm_a783f3b2734d186aff2a9619e88636bcb}{{\bfseries select\-Segs} segments}\label{classCharmm_a783f3b2734d186aff2a9619e88636bcb}

\item 
\hypertarget{classCharmm_a2b46b343750f7e9097d194b439f9bb50}{{\bfseries get\-Replacable} args}\label{classCharmm_a2b46b343750f7e9097d194b439f9bb50}

\item 
\hypertarget{classCharmm_af14591e93cac0f62b317605d794d5067}{{\bfseries search} fname}\label{classCharmm_af14591e93cac0f62b317605d794d5067}

\item 
\hypertarget{classCharmm_acd6d759656ff972b0a362f59f73f8bd1}{{\bfseries load} type fname}\label{classCharmm_acd6d759656ff972b0a362f59f73f8bd1}

\item 
\hypertarget{classCharmm_a59d83144833bf97dd3541eff035ad94e}{{\bfseries addseg} segid seq}\label{classCharmm_a59d83144833bf97dd3541eff035ad94e}

\item 
\hypertarget{classCharmm_a89480e4e8c46045350f163802d6193c2}{{\bfseries build2nd\-Struct} segid?type??start??end?}\label{classCharmm_a89480e4e8c46045350f163802d6193c2}

\item 
\hypertarget{classCharmm_a71efa5014df03cb9e2dde4cb6fc5a25b}{{\bfseries querylength} segid}\label{classCharmm_a71efa5014df03cb9e2dde4cb6fc5a25b}

\item 
\hypertarget{classCharmm_a03e1c86b1cabf415e13302172e994c1f}{{\bfseries run} setup?configuration?}\label{classCharmm_a03e1c86b1cabf415e13302172e994c1f}

\item 
\hypertarget{classCharmm_a3e116a7cb52bf3bd101fd473e4d343cd}{{\bfseries complete} setup?configuration?}\label{classCharmm_a3e116a7cb52bf3bd101fd473e4d343cd}

\item 
\hypertarget{classCharmm_aec97d9b7b04a546306a024446223127f}{{\bfseries continue} setup1 with setup2?configuration?}\label{classCharmm_aec97d9b7b04a546306a024446223127f}

\item 
\hypertarget{classCharmm_a4cdb90a0bfc675ca5c45a9b0bd9e70bc}{{\bfseries redo} setup?configuration?}\label{classCharmm_a4cdb90a0bfc675ca5c45a9b0bd9e70bc}

\item 
\hypertarget{classCharmm_a52c0e353aaf9cf3d222a5eb87790133d}{{\bfseries get\-Segments}}\label{classCharmm_a52c0e353aaf9cf3d222a5eb87790133d}

\item 
\hypertarget{classCharmm_a8002064dad06e7f20d3d38ed57fd8d2a}{{\bfseries rename\-Segment} \-A \-B}\label{classCharmm_a8002064dad06e7f20d3d38ed57fd8d2a}

\item 
\hypertarget{classCharmm_a6ef2fecce6d31cff7bc9a4a5281b3d34}{{\bfseries generate}}\label{classCharmm_a6ef2fecce6d31cff7bc9a4a5281b3d34}

\item 
\hypertarget{classCharmm_a45037b5bafc6bd6125e9f1081e866d11}{{\bfseries process\-Psf}}\label{classCharmm_a45037b5bafc6bd6125e9f1081e866d11}

\item 
\hypertarget{classCharmm_a99ed51fa0b17e883d23c85ddc08b05a2}{{\bfseries set\-Solvent} solvation\-\_\-model?configuration?}\label{classCharmm_a99ed51fa0b17e883d23c85ddc08b05a2}

\end{DoxyCompactItemize}


\-The documentation for this class was generated from the following files\-:\begin{DoxyCompactItemize}
\item 
core/\-Charmm.\-tcl\item 
modules/conf/\-I\-C.\-tcl\item 
modules/energy/energy.\-tcl\item 
modules/geo/cons.\-tcl\item 
modules/geo/\hyperlink{geo_8tcl}{geo.\-tcl}\item 
modules/\-I\-O/\-I\-O.\-tcl\item 
modules/\-I\-O/manipulation.\-tcl\item 
modules/\-M\-D/\-M\-D.\-tcl\item 
modules/sequence/segment.\-tcl\item 
modules/solvation/implicit.\-tcl\end{DoxyCompactItemize}
